Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly

被引:21
作者
Dutilh, Bas E. [1 ]
Huynen, Martijn A. [1 ]
Strous, Marc [2 ,3 ,4 ]
机构
[1] Radboud Univ Nijmegen, Med Ctr, Nijmegen Ctr Mol Life Sci, Ctr Mol & Biomol Informat, NL-6525 GA Nijmegen, Netherlands
[2] MPI Marine Microbiol, D-28359 Bremen, Germany
[3] Radboud Univ Nijmegen, Dept Microbiol, NL-6525 AJ Nijmegen, Netherlands
[4] Univ Bielefeld, Ctr Biotechnol, D-4800 Bielefeld, Germany
关键词
GENERATION; SEQUENCES; BACTERIA;
D O I
10.1093/bioinformatics/btp377
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Motivation: Most microbial species can not be cultured in the laboratory. Metagenomic sequencing may still yield a complete genome if the sequenced community is enriched and the sequencing coverage is high. However, the complexity in a natural population may cause the enrichment culture to contain multiple related strains. This diversity can confound existing strict assembly programs and lead to a fragmented assembly, which is unnecessary if we have a related reference genome available that can function as a scaffold. Results: Here, we map short metagenomic sequencing reads from a population of strains to a related reference genome, and compose a genome that captures the consensus of the population's sequences. We show that by iteration of the mapping and assembly procedure, the coverage increases while the similarity with the reference genome decreases. This indicates that the assembly becomes less dependent on the reference genome and approaches the consensus genome of the multi-strain population.
引用
收藏
页码:2878 / 2881
页数:4
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